Tip of the Week: ENCODE data at UCSC

encode_standaloneENCODE stand for Encyclopedia of DNA Elements.  This is a major project to examine the sequence elements of the human genome in extensive detail, involving many groups in the US and beyond,  coordinated and sponsored by the NHGRI.  Last year as this was brewing I did a series of “Tips of the Week” about the ENCODE data that included the pilot project and the production phase data that is being wrangled by the folks at the UCSC Genome Browser and displayed in that framework.  Well, now that data is rolling in, and and you have access to the pre-publication data being generated. In this Tip of the Week we offer background on the project and look specifically at some of that data.

We have created a more formal presentation for this which you can watch here as a stand-alone movie.  It is longer than we usually have as a “tip”, but we think it is important to understand the background and foreground to understand how to get the most out of the data.

Congratulations to the ENCODE DCC team at UCSC that is led by Kate Rosenbloom for making this data available.  And thanks to the ENCODE project teams for generating this data.

This material is also embedded in our complete package of UCSC materials that are freely available here.  If you aren’t already familiar with the UCSC Genome Browser you may want to explore that first.  The ENCODE piece is a segment of the “Additional Tools” tutorial.  All of our slides are there and you can download and use the slides to teach students.  There is also an exercise that walks you through a sample of the data in the exercise download.

As more pieces of the project come along we expect to enhance this movie and it will touch on many of the data types available as part of this large project.  We’ll add additional exercises.  We hope you can make use of the hot-off-the-projects (before the presses!) data that can help your research.

ENCODE at NHGRI: http://www.genome.gov/10005107

ENCODE DCC site: http://genome.ucsc.edu/ENCODE/

Complete training suite on UCSC Genome Browser (ENCODE portion is in the Associated Tools section at this time): http://www.openhelix.com/cgi/tutorialInfo.cgi?id=76

ENCODE data at UCSC stand-alone movie direct link: http://www.openhelix.com/downloads/jing/encode/encode_movie.html

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